Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboos
image: Patterns of subgenome and allelic gene expression. (A) Cytokinin (CTK)-induced in vitro flowering and auxin (IAA)-induced in vitro rejuvenation of B. odashimae. The pictures from left to right represent the vegetative shoots, flowering shoots, and flower anatomy of B. odashimae, respectively. (B) PCA of the first two principal components of subgenome expression profiles across 11 different developmental stages under different hormone treatments. (C) PCA plot of the first two principal components of allele expression profiles across 11 stages. (D) Transcript abundance across all samples for expressed genes among subgenome A, B, and C of Hap I. (E) Transcript abundance across all samples for expressed genes among Hap I, Hap II, and Hap III. (F) The violin plot of biased expression for homoeologous genes of subgenome A and subgenome C across all samples. (G) Proportions of alleles with allelic expression bias across 11 different samples. There are three categories: small allele expression differences (ASE) genes, large ASE genes, and balanced genes without difference. (H) Absolute expression abundance for the small ASE genes (left) and large ASE genes (right). (I) Distances to the nearest TEs of small ASE genes (left) and large ASE (right). (J) Analysis of the number of differentially expressed genes among different haplotype pairs. (K) Distances to the nearest TEs for large ASE in different haplotypes. The line in the center of each plot (D, E, F, H, I, J, and K) represents the median value, and the bounds of each box indicate the first (25%) and third (75%) quartiles. Mann–Whitney–Wilcoxon test. *P < 0.05; **P < 0.01; ***P < 0.001 and ****P < 0.0001.
Credit: Horticulture Research
Bamboo flowering is a rare and enigmatic event, especially in woody species that flower only once in decades. In this study, researchers decoded the complex, haplotype-resolved genome of Bambusa odashimae, a nonaploid bamboo species known for its ability to flower in vitro. The team identified three distinct haplotypes with different parental origins and revealed extensive allele-specific expression linked to hormonal responses. Key flowering regulators such as CONSTANS (CO) genes showed differential expression under cytokinin and auxin treatments. These insights provide a critical step forward in understanding how polyploidy and hybridization influence flowering and rejuvenation in bamboos, offering a new model for genetic studies in perennial woody plants.
Woody bamboos, despite their ecological and economic value, exhibit infrequent and unpredictable flowering, often followed by plant death. This unique flowering behavior is tied to their polyploid nature and complex evolutionary history, including interspecific and intergeneric hybridization. Most flowering research has focused on diploid or tetraploid plants, leaving the mechanisms in highly polyploid species largely unknown. Bambusa odashimae stands out for both its unusually high chromosome number (104) and its ability to flower and regenerate under tissue culture. Due to these challenges, it is necessary to conduct in-depth studies on flowering mechanisms in polyploid bamboos.
A research team from the Kunming Institute of Botany, Chinese Academy of Sciences, published a study (DOI: 10.1093/hr/uhae250) on September 4, 2024, in Horticulture Research, unveiling a haplotype-resolved, chromosome-level genome of B. odashimae. The study combined Nanopore, Hi-C, and transcriptome sequencing from 11 developmental stages to explore the genomic basis of in vitro flowering. Their work revealed the hybrid origin of the species and identified key hormonal pathways and transcriptional regulators involved in flowering, providing an important model for polyploidy and hormone-mediated plant development.
The researchers assembled a 3.36 Gb genome of B. odashimae, resolving it into three haplotypes—Hap I (from Dendrocalamus) and Hap II and III (from Bambusa species). Each haplotype contained A, B, and C subgenomes, exhibiting structural variation and distinct gene expression patterns. Notably, 40% of the genes displayed large allele-specific expression (ASE), particularly enriched in cytokinin-related pathways during flowering induction.
Cytokinin treatment triggered in vitro flowering, while auxin induced vegetative rejuvenation. Transcriptomic profiling revealed that cytokinin upregulated several key regulators, including CKX9, RR8, and RR4, with expression bias across alleles. In contrast, auxin reversed these effects, promoting rejuvenation. Further, the team identified six CONSTANS (CO) alleles, with BodCO_4, BodCO_5, and BodCO_6 showing hormone-responsive expression. These alleles had a unique 11-amino acid deletion and specific cis-regulatory elements, suggesting functional divergence from BodCO_1–3. Co-expression network analysis linked CO and COL genes to circadian and hormone pathways, offering a mechanism by which cytokinin represses CO expression to induce flowering. The study also showed that intergeneric hybridization (e.g., Hap I vs. Hap II/III) contributed more to ASE than interspecific hybridization, underscoring hybrid origin as a key factor in transcriptional complexity.
“This study represents a significant leap in our understanding of bamboo biology,” says Dr. Peng-Fei Ma, co-corresponding author of the study. “By resolving the haplotypes of a nonaploid species and tracking gene expression during flowering and regeneration, we now have a framework for exploring how hybridization and polyploidy shape plant development. Our findings not only unravel part of the bamboo flowering mystery but also provide a valuable genomic resource for future studies.”
This research provides a foundational platform for genetic studies and breeding in bamboos, particularly those with complex polyploid genomes. Understanding the molecular control of flowering could help in regulating bamboo’s life cycle, benefiting industries that rely on consistent shoot production. The insights into hormone-responsive genes and ASE also open doors for manipulating flowering time through biotechnology. More broadly, the combination of a haplotype-resolved genome and in vitro flowering system makes B. odashimae a powerful model for studying allopolyploid evolution, gene dosage effects, and developmental plasticity in perennial woody plants.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae250
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.